How to soft-clip in SAMTOOLS?

[kirito]

Hello everyone,

I am using SAMTOOLS to view, sort, and index parts of a patient's DNA. But no matter what I do, I always get the same answer in alignment of this DNA with reference DNA: "empty."

I think the problem is that I don't have my data soft-clipped. How do I soft-clip data in samtools? Does samtools sort do soft-clipping? Because I already use samtools sort. Thanks!

[westerman]

As far as I know Samtools does not do soft-clipping. It does have the CIGAR string which will contain clipping information.

Since you are new person to SeqAnswers I have to ask the basic question: You do know that Samtools does not do alignment? Rather it parses sam/bam files that other alignment programs have created. If the up-stream alignment program did not find an alignment then Samtools can not report an alignment.

[chadn737]

Soft-clipping is done by some alignment software (BWA and bowtie2) during the initial alignment. I'm not sure what you are asking otherwise.

[Heisman]

We need to have a mandatory sticky that should be read and quizzed over prior to asking questions. Your post makes little sense to me. Please copy and paste all of the commands you used as well as the error message you saw. Samtools does not perform softcliipping; I am not aware of any non-aligner tools that do (although there may be some).

[kirito]

Yes, I do know that samtools does not do alignment. I am using another program called SHEAR to do that. However, when I run my files through SHEAR, all the results end up being "empty". This would mean two things in my opinion: 1) the data I have does not have any differences with the reference genome, or 2) there is a problem with the data. I ran the data again through CREST (which detects genetic structural variations), and the result came up as empty again. CREST informed me that I needed to have soft-clipped data.

[westerman]

Yes, I do know that samtools does not do alignment. I am using another program called SHEAR to do that.

Never heard of the program. The seqanswers wiki page on known software does not list it. Could you give a reference to the program? Ditto with CREST.

However, when I run my files through SHEAR, all the results end up being "empty". This would mean two things in my opinion: 1) the data I have does not have any differences with the reference genome, or 2) there is a problem with the data. I ran the data again through CREST (which detects genetic structural variations), and the result came up as empty again. CREST informed me that I needed to have soft-clipped data.

Usually an alignment needs to be made before detecting variants.

[dpryan]

Why don't you just realign the data with an aligner that does soft-clipping (many aligners don't do that by default)? Trying to soft-clip after the fact is a fool's errand.